pcr buffer Search Results


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  • 99
    New England Biolabs phusion high fidelity pcr master mix
    Agarose gel electrophoresis analysis of <t>PCR</t> fragments multiplied by <t>Phusion</t> High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.
    Phusion High Fidelity Pcr Master Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4975 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher pcr buffer
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
    Pcr Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 29048 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher 1x pcr buffer
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
    1x Pcr Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 3634 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega pcr buffer
    <t>DNA</t> extraction, <t>PCR</t> amplification, sequencing, and analysis.
    Pcr Buffer, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 7741 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore pcr buffer
    Methylation status of the Sox17 promoter in breast cancer tissues and paired plasma <t>DNA.</t> (A) Representative results of MSP assays of Sox17 methylation in primary breast cancer tissues; B. Representative results of MSP of Sox17 methylation in paired plasma DNA. DW = distilled water, M = methylated, MSP = methylation-specific polymerase chain reaction, NC = negative control, P = plasma DNA, PC = positive control, T = breast cancer tissue, U = unmethylated.
    Pcr Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 2561 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher 10x pcr buffer
    Methylation status of the Sox17 promoter in breast cancer tissues and paired plasma <t>DNA.</t> (A) Representative results of MSP assays of Sox17 methylation in primary breast cancer tissues; B. Representative results of MSP of Sox17 methylation in paired plasma DNA. DW = distilled water, M = methylated, MSP = methylation-specific polymerase chain reaction, NC = negative control, P = plasma DNA, PC = positive control, T = breast cancer tissue, U = unmethylated.
    10x Pcr Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 2258 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher pcr buffer ii
    Inactivation of <t>MVA-VP2</t> by heat or UV irradiation . Agarose gel electrophoresis of <t>RT-PCR</t> product of the AHSV-VP2 gene transcripts. DF-1 cells were infected with live, purified, heat or UV irradiated MVA-VP2 and 48 h later, VP2-mRNA detection was performed by RT-PCR.
    Pcr Buffer Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 2070 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher pcr reaction buffer
    Polymorphism of four VNTRs . The polymorphism of VNTRs (SAG2, SAG3, SAG4 and SAG22) is shown by agarose gel electrophoresis of <t>PCR</t> products. The first strain on each gel is the reference strain and the PCR products were loaded alongside a 100 bp <t>DNA</t> size ladder (the sizes in base pairs are shown on the left side of the first panel). The allele number, corresponding to the number of repeats, is indicated under the band.
    Pcr Reaction Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5738 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Meridian Life Science pcr buffer
    DGGE analysis of nested 160-bp β-proteobacterial ammonia oxidizer 16S rDNA sequences amplified from <t>DNA</t> extracted from Loch Duich marine sediments and reference sequences retrieved from Loch Duich sediments by cloning and by sequencing of excised DGGE bands. Lanes: EL, environmental library (DGGE sequences excised and reamplified from 357f-GC plus 518r 16S rDNA <t>PCR</t> products); CL, clone library (βAMO161f plus βAMO1301 clone sequences retrieved from Loch Duich sediments and reamplified with 357f-GC plus 518r for DGGE analysis); 1 to 40, depth profile of Loch Duich 16S rDNA 357f-GC plus 518r PCR products. Clone sequences shown in lane CL are (from top to bottom) LD1-B6, LD1-B37, LD1-A40, LD1-A3, LD1-A1, LD1-A2, LD1-B20, LD1-B10, LD1-B28, LD1-A10, LD1-A15, LD1-B9, and LD1-A20; DGGE excised sequences shown in lane EL are (from top to bottom) LD1-env-A12, LD1-env-B12, LD1-env-B11, LD1-env-B5, LD1-env-A8, LD1-env-A5, LD1-env-A1, and LD1-env-A2. Arrows (right) mark the prominent bands as referred to in the text. No sequence was generated from band X when it was excised and reamplified.
    Pcr Buffer, supplied by Meridian Life Science, used in various techniques. Bioz Stars score: 94/100, based on 2148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher pcr gold buffer
    Detecting murine <t>DNA</t> by IAP <t>PCR.</t> PCR products were analyzed on 1.5% agarose gels containing ethidium bromide. (A) Sensitivity of the IAP PCR assay was determined by performing PCRs on titrations of EL4 murine cell line DNA in a background of 200 ng LNCaP DNA. One murine cell equivalent (1 eq) indicates 6 pg of EL4 DNA. XMRV-infected LNCaP (iLNCaP) and uninfected LNCaP (uLNCaP) were included as controls. (B) Screening results for 17 HIV-1 + patient samples. Arrow points to sample 103219, which tested positive for XMRV by non-nested gag PCR. (m) 100 base pair molecular weight marker, (EL4) 6 pg of murine EL4 cell line DNA without a background of human DNA.
    Pcr Gold Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1161 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa pcr buffer
    <t>PCR</t> amplification of total <t>DNA</t> of Arabidopsis
    Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 10602 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen onestep rt pcr buffer
    <t>PCR</t> amplification of total <t>DNA</t> of Arabidopsis
    Onestep Rt Pcr Buffer, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 695 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs phusion high fidelity pcr master mix with hf buffer
    <t>PCR</t> amplification of total <t>DNA</t> of Arabidopsis
    Phusion High Fidelity Pcr Master Mix With Hf Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 567 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega pcr amplification
    <t>PCR</t> amplification of <t>Rbcl</t> after cutting using HaeIII and BlgII enzymes, where E1 to E3 different Egyptian cotton varieties A1 to A3 are different American cotton varieties and the L is lab’s cotton. The white arrows show some bands differentiate between Egyptian and American genotypes:
    Pcr Amplification, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 15387 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Boehringer Mannheim pcr buffer
    Gel electrophoresis (2% TAE-agarose gel) showing amplified DNA of potentially contaminated samples (specific bands of approximately 500-bp length). Lanes: 1, 100-bp marker; 2, zymolyase, contaminated lot; 3, zymolyase, contaminated lot, 1:10 dilution; 4, <t>10×</t> buffer from digoxigenin (Dig)-labeling kit (Boehringer Mannheim), contaminated lot; 5, 10× buffer from Dig-labeling kit (Boehringer Mannheim), contaminated lot; 6, zymolyase, regular lot, not contaminated; 7, proteinase K, regular lot, not contaminated; 8, lyticase, contaminated lot; 9, lysing enzyme extracted from T. harzianum ; 10, positive control, A. fumigatus DNA, extracted from 10 3 CFU; 11, negative control of the extraction; and 12, negative control of the <t>PCR.</t>
    Pcr Buffer, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 959 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare pcr buffer
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    Pcr Buffer, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 99/100, based on 994 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega 1x pcr buffer
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    1x Pcr Buffer, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 1017 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore 10x pcr buffer
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    10x Pcr Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 223 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher accuprime pcr buffer ii
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    Accuprime Pcr Buffer Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 445 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore 1x pcr buffer
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    1x Pcr Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 311 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher geneamp pcr buffer ii
    Gel images illustrating the quality of RNA extracts and their suitability for <t>RT-PCR.</t> In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii <t>nifH</t> RT-PCR products (370 bp; 2% agarose).
    Geneamp Pcr Buffer Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 368 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Agarose gel electrophoresis analysis of PCR fragments multiplied by Phusion High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.

    Journal: Scientific Reports

    Article Title: High-throughput mutagenesis using a two-fragment PCR approach

    doi: 10.1038/s41598-017-07010-4

    Figure Lengend Snippet: Agarose gel electrophoresis analysis of PCR fragments multiplied by Phusion High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.

    Article Snippet: PCR set-up and high-throughput mutagenesis PCR conditions were first tested for a random set of 30 CB2 mutants using Phusion High-Fidelity PCR Master Mix with HF Buffer, Phusion High-Fidelity PCR Master Mix with GC Buffer (New England Biolabs, NEB) and KOD Hot Start Master Mix (Merck Millipore).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Mutagenesis

    Comparison of PCR and Southern hybridization results for four representative V. parahaemolyticus strains. (A) tdh detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic

    Journal: Infection and Immunity

    Article Title: Vibrio parahaemolyticus Disruption of Epithelial Cell Tight Junctions Occurs Independently of Toxin Production

    doi: 10.1128/IAI.73.3.1275-1283.2005

    Figure Lengend Snippet: Comparison of PCR and Southern hybridization results for four representative V. parahaemolyticus strains. (A) tdh detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic

    Article Snippet: The tdh and tlh PCR mixtures (final volume, 25 μl) contained 10× PCR buffer (50 mM KCl, 10 mM Tris [pH 8.5], 0.1% gelatin, 1.5% MgCl2 ), each deoxynucleoside triphosphate (Invitrogen Life Technologies, Burlington, Ontario, Canada) at a concentration of 0.25 mM, Taq polymerase (1.25 U; New England Biolabs Ltd., Mississauga, Ontario, Canada), and nuclease-free water (Gibco).

    Techniques: Polymerase Chain Reaction, Hybridization

    Distribution of genes among saprophytic and pathogenic leptospires. Genomic DNA from L. biflexa Patoc and from ten serovars belonging to the pathogenic species of Leptospira were subjected to PCR analysis with specific primers designed according to L. interrogans serovar Copenhageni genome sequences. ( A ) Amplification of 16S DNA shows template integrity; ( B ) LIC10821 and ( C ) LIC10672. No DNA was added to the negative control reaction (-).

    Journal: The Open Microbiology Journal

    Article Title: Evaluation of Immunoprotective Activity of Six Leptospiral Proteins in the Hamster Model of Leptospirosis

    doi: 10.2174/1874285801206010079

    Figure Lengend Snippet: Distribution of genes among saprophytic and pathogenic leptospires. Genomic DNA from L. biflexa Patoc and from ten serovars belonging to the pathogenic species of Leptospira were subjected to PCR analysis with specific primers designed according to L. interrogans serovar Copenhageni genome sequences. ( A ) Amplification of 16S DNA shows template integrity; ( B ) LIC10821 and ( C ) LIC10672. No DNA was added to the negative control reaction (-).

    Article Snippet: PCR was performed in a reaction volume of 25 μl containing 100 ng of genomic DNA, 1 X PCR buffer (20 mM Tris-HCl, pH 8.4, 50 mM KCl), 2 mM MgCl2 , 20 pmol of each specific primer, 200 μM of each dNTP, and 2.5 U Taq DNA Polymerase (Invitrogen).

    Techniques: Polymerase Chain Reaction, Amplification, Negative Control

    Haematoxylin/eosin (H E)-staining of historical formalin-fixed paraffin-embedded (FFPE) mouse kidney necropsy samples from the University of North Carolina, Chapel Hill, USA and Israel, paired with agarose gels of 25 cycle 869–870 PCR for MKPV DNA using DNA extracted from FFPE kidney shavings of necropsies from the same sites. For the Israel specimen, ISH for MKPV nucleic acids was also performed. Arrows show examples of inclusion bodies in each H E stain. PCR panels include size markers at left (0.1–1.0 kb, in 0.1 kb increments) and control DNA at right from MKPV-infected Centenary Institute Rag1 –/– mice (+ve) or MKPV-free Rag1 –/– mice (-ve, sourced from Australian BioResources, Mittagong NSW).

    Journal: PLoS Pathogens

    Article Title: Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys

    doi: 10.1371/journal.ppat.1008262

    Figure Lengend Snippet: Haematoxylin/eosin (H E)-staining of historical formalin-fixed paraffin-embedded (FFPE) mouse kidney necropsy samples from the University of North Carolina, Chapel Hill, USA and Israel, paired with agarose gels of 25 cycle 869–870 PCR for MKPV DNA using DNA extracted from FFPE kidney shavings of necropsies from the same sites. For the Israel specimen, ISH for MKPV nucleic acids was also performed. Arrows show examples of inclusion bodies in each H E stain. PCR panels include size markers at left (0.1–1.0 kb, in 0.1 kb increments) and control DNA at right from MKPV-infected Centenary Institute Rag1 –/– mice (+ve) or MKPV-free Rag1 –/– mice (-ve, sourced from Australian BioResources, Mittagong NSW).

    Article Snippet: DNA was screened for DrPV-1 sequences using Platinum Taq DNA polymerase and high fidelity PCR buffer (Invitrogen), primers Chap-DRPv-fwd and Chap-DRPv-rev, an initial temperature of 94˚C for 0.5 min, and 35 cycles of 94˚C for 0.25 min, 57˚C for 0.5 min and 68˚C for 1 min. Products were resolved by agarose gel electrophoresis.

    Techniques: Staining, Formalin-fixed Paraffin-Embedded, Polymerase Chain Reaction, In Situ Hybridization, Infection, Mouse Assay

    Map of the MKPV genome. (A-B) Maps of the MKPV/MuCPV strains from Centenary Institute (CI, accession MH670587), Memorial Sloan Kettering Cancer Center (MSKCC, accession MH670588) and New York City basements (wild-NY, MF175078). “Bowties” indicate terminal repeats (TR). (A) Single nucleotide variations (SNV) between the CI, MSKCC and wild-NY accessions. Vertical lines—differences between accessions. Half height vertical lines—polymorphisms within an accession. ▼; 2 bp insertion in the CI strain. ▲; 1 bp insertion in a CI sub-strain. Dashed lines—missing extremities in MSKCC and wild-NY accessions, which consist of the exterior inverted repeats in the full-length CI sequence. (B-C) Alternative splicing allows production of the polypeptides p10, p15, NS1, NS2, NP and VP. Black, brown or blue shading indicate the relative reading frames of ORFs. p15, p10 and NP could theoretically be produced from multiple transcripts. Orange or red indicate peptides present in LC-MS/MS datasets PXD014938 (this paper) or PXD010540 [ 9 ], respectively. Exon or intron sequences flanking splice sites are shown in black or red text, respectively. (C) Quantitation of spliced MKPV reads in RNAseq data pooled from two MKPV-infected kidneys. Columns indicate splice site usage (left y-axis); heights of arcs (right y-axis) indicate the abundance of specific splice combinations. See S4 Table for more information. (D-E) Detection of spliced transcripts by RT-dependent PCR, using primers mapped in A-B. Input templates were MKPV-infected (D) kidney DNA or (E) DNAse/ExoI-treated kidney RNA, converted (+RT) or mock-converted (-RT) to cDNA. RT-PCR products corresponding to transcripts 1 to 4 are indicated by white numbers. (F) Mapping of transcription start and stop sites by RACE. See S1 Fig for RACE details. Major 5’ and 3’ RACE products, indicated by black arrows and corresponding to transcripts 2 to 4 or polyadenylation signals A and B, were gel-purified and Sanger sequenced. Other RACE products mentioned in the text are indicated by white arrows.

    Journal: PLoS Pathogens

    Article Title: Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys

    doi: 10.1371/journal.ppat.1008262

    Figure Lengend Snippet: Map of the MKPV genome. (A-B) Maps of the MKPV/MuCPV strains from Centenary Institute (CI, accession MH670587), Memorial Sloan Kettering Cancer Center (MSKCC, accession MH670588) and New York City basements (wild-NY, MF175078). “Bowties” indicate terminal repeats (TR). (A) Single nucleotide variations (SNV) between the CI, MSKCC and wild-NY accessions. Vertical lines—differences between accessions. Half height vertical lines—polymorphisms within an accession. ▼; 2 bp insertion in the CI strain. ▲; 1 bp insertion in a CI sub-strain. Dashed lines—missing extremities in MSKCC and wild-NY accessions, which consist of the exterior inverted repeats in the full-length CI sequence. (B-C) Alternative splicing allows production of the polypeptides p10, p15, NS1, NS2, NP and VP. Black, brown or blue shading indicate the relative reading frames of ORFs. p15, p10 and NP could theoretically be produced from multiple transcripts. Orange or red indicate peptides present in LC-MS/MS datasets PXD014938 (this paper) or PXD010540 [ 9 ], respectively. Exon or intron sequences flanking splice sites are shown in black or red text, respectively. (C) Quantitation of spliced MKPV reads in RNAseq data pooled from two MKPV-infected kidneys. Columns indicate splice site usage (left y-axis); heights of arcs (right y-axis) indicate the abundance of specific splice combinations. See S4 Table for more information. (D-E) Detection of spliced transcripts by RT-dependent PCR, using primers mapped in A-B. Input templates were MKPV-infected (D) kidney DNA or (E) DNAse/ExoI-treated kidney RNA, converted (+RT) or mock-converted (-RT) to cDNA. RT-PCR products corresponding to transcripts 1 to 4 are indicated by white numbers. (F) Mapping of transcription start and stop sites by RACE. See S1 Fig for RACE details. Major 5’ and 3’ RACE products, indicated by black arrows and corresponding to transcripts 2 to 4 or polyadenylation signals A and B, were gel-purified and Sanger sequenced. Other RACE products mentioned in the text are indicated by white arrows.

    Article Snippet: DNA was screened for DrPV-1 sequences using Platinum Taq DNA polymerase and high fidelity PCR buffer (Invitrogen), primers Chap-DRPv-fwd and Chap-DRPv-rev, an initial temperature of 94˚C for 0.5 min, and 35 cycles of 94˚C for 0.25 min, 57˚C for 0.5 min and 68˚C for 1 min. Products were resolved by agarose gel electrophoresis.

    Techniques: Sequencing, Produced, Liquid Chromatography with Mass Spectroscopy, Quantitation Assay, Infection, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Purification

    DNA extraction, PCR amplification, sequencing, and analysis.

    Journal: Applied and Environmental Microbiology

    Article Title: Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems

    doi: 10.1128/AEM.01097-15

    Figure Lengend Snippet: DNA extraction, PCR amplification, sequencing, and analysis.

    Article Snippet: PCR analysis was performed in 50-μl reaction mixtures that contained 2 μl of the extracted DNA, 1× PCR buffer (Promega, Madison, WI), 2.5 mM MgSO4 , a 0.2 mM deoxyribonucleoside triphosphate (dNTP) mixture, 0.5 U of GoTaq flexi DNA polymerase (Promega, Madison, WI), and a 10 μM concentration of each of the forward and reverse primers.

    Techniques: DNA Extraction, Polymerase Chain Reaction, Amplification, Sequencing

    Methylation status of the Sox17 promoter in breast cancer tissues and paired plasma DNA. (A) Representative results of MSP assays of Sox17 methylation in primary breast cancer tissues; B. Representative results of MSP of Sox17 methylation in paired plasma DNA. DW = distilled water, M = methylated, MSP = methylation-specific polymerase chain reaction, NC = negative control, P = plasma DNA, PC = positive control, T = breast cancer tissue, U = unmethylated.

    Journal: Medicine

    Article Title: Sox17 Promoter Methylation in Plasma DNA Is Associated With Poor Survival and Can Be Used as a Prognostic Factor in Breast Cancer

    doi: 10.1097/MD.0000000000000637

    Figure Lengend Snippet: Methylation status of the Sox17 promoter in breast cancer tissues and paired plasma DNA. (A) Representative results of MSP assays of Sox17 methylation in primary breast cancer tissues; B. Representative results of MSP of Sox17 methylation in paired plasma DNA. DW = distilled water, M = methylated, MSP = methylation-specific polymerase chain reaction, NC = negative control, P = plasma DNA, PC = positive control, T = breast cancer tissue, U = unmethylated.

    Article Snippet: Each MSP reaction included 2 μL of DNA template, 0.18 μL of each primer, 0.45 μL of 10 mM dNTP Mix (Promega Corp., Madison, WI, USA) 1.5 μL 10× PCR buffer, and 0.12 μL of HotStart Taq DNA Polymerase (Sigma, Germany) in a final reaction volume of 15 μL.

    Techniques: Methylation, Polymerase Chain Reaction, Negative Control, Positive Control

    Inactivation of MVA-VP2 by heat or UV irradiation . Agarose gel electrophoresis of RT-PCR product of the AHSV-VP2 gene transcripts. DF-1 cells were infected with live, purified, heat or UV irradiated MVA-VP2 and 48 h later, VP2-mRNA detection was performed by RT-PCR.

    Journal: Antiviral Research

    Article Title: The immunogenicity of recombinant vaccines based on modified Vaccinia Ankara (MVA) viruses expressing African horse sickness virus VP2 antigens depends on the levels of expressed VP2 protein delivered to the host

    doi: 10.1016/j.antiviral.2018.04.015

    Figure Lengend Snippet: Inactivation of MVA-VP2 by heat or UV irradiation . Agarose gel electrophoresis of RT-PCR product of the AHSV-VP2 gene transcripts. DF-1 cells were infected with live, purified, heat or UV irradiated MVA-VP2 and 48 h later, VP2-mRNA detection was performed by RT-PCR.

    Article Snippet: Amplification of the VP2 gene was performed by PCR using PCR Buffer II (Invitrogen), dNTPs, specific primers (forward and reverse primers), MgCl2 solution, AmpliTaq DNA Polymerase (Invitrogen), and cDNA template.

    Techniques: Irradiation, Agarose Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Infection, Purification

    Polymorphism of four VNTRs . The polymorphism of VNTRs (SAG2, SAG3, SAG4 and SAG22) is shown by agarose gel electrophoresis of PCR products. The first strain on each gel is the reference strain and the PCR products were loaded alongside a 100 bp DNA size ladder (the sizes in base pairs are shown on the left side of the first panel). The allele number, corresponding to the number of repeats, is indicated under the band.

    Journal: BMC Microbiology

    Article Title: A multi locus variable number of tandem repeat analysis (MLVA) scheme for Streptococcus agalactiae genotyping

    doi: 10.1186/1471-2180-11-171

    Figure Lengend Snippet: Polymorphism of four VNTRs . The polymorphism of VNTRs (SAG2, SAG3, SAG4 and SAG22) is shown by agarose gel electrophoresis of PCR products. The first strain on each gel is the reference strain and the PCR products were loaded alongside a 100 bp DNA size ladder (the sizes in base pairs are shown on the left side of the first panel). The allele number, corresponding to the number of repeats, is indicated under the band.

    Article Snippet: PCR was performed in a final volume of 25 μl containing 10 ng DNA, 1 × PCR Reaction Buffer, 2 mM MgCl2 (Applied Biosystems), 5% DMSO (dimethyl sulfoxide), 1 unit of Taq DNA polymerase (Applied Biosystems), 200 μM of each dNTP and 0.5 μM of each flanking primer (Eurogentec, Belgium).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction

    Histone modifications associated with an in vitro methylated MAGEA1 transgene. A , Schematic representation of the structure and DNA methylation status of the active unmethylated (empty circles) MAGEA1 gene and the inactive methylated (filled circles) MAGEA1/hph transgene in MZ2-MEL.TrHM cells. Black boxes correspond to the MAGEA1 exons, the dark gray box within the MAGEA1/hph transgene represents the hph transcription unit, and the asterisk (*) is the site where a 12-bp tag sequence (carrying a Xba I restriction site) was inserted. The lower panel is an enlargement of the amplicon that was amplified in ChIP experiments, and indicates the expected fragment sizes following Xba I digestion. B , ChIP experiments were applied to MZ2-MEL.TrHM. The resulting MAGEA1 amplicons were digested with Xba I and separated on agarose gels, thereby revealing relative enrichment of the indicated histone modifications within either the MAGEA1 gene (upper band) or the MAGEA1/hph transgene (lower band). C , Relative enrichment of histone marks on the transgene was deduced by quantifying band intensities in gel electrophoresis pictures (ImageJ software), and calculating the lower/upper ratio. Data, which were normalized by the lower/upper ratio in input samples, derive from at least two independent ChIP experiments, with two PCR/XbaI/electrophoresis analyses in each case. * P

    Journal: PLoS ONE

    Article Title: Epigenetic Hierarchy within the MAGEA1 Cancer-Germline Gene: Promoter DNA Methylation Dictates Local Histone Modifications

    doi: 10.1371/journal.pone.0058743

    Figure Lengend Snippet: Histone modifications associated with an in vitro methylated MAGEA1 transgene. A , Schematic representation of the structure and DNA methylation status of the active unmethylated (empty circles) MAGEA1 gene and the inactive methylated (filled circles) MAGEA1/hph transgene in MZ2-MEL.TrHM cells. Black boxes correspond to the MAGEA1 exons, the dark gray box within the MAGEA1/hph transgene represents the hph transcription unit, and the asterisk (*) is the site where a 12-bp tag sequence (carrying a Xba I restriction site) was inserted. The lower panel is an enlargement of the amplicon that was amplified in ChIP experiments, and indicates the expected fragment sizes following Xba I digestion. B , ChIP experiments were applied to MZ2-MEL.TrHM. The resulting MAGEA1 amplicons were digested with Xba I and separated on agarose gels, thereby revealing relative enrichment of the indicated histone modifications within either the MAGEA1 gene (upper band) or the MAGEA1/hph transgene (lower band). C , Relative enrichment of histone marks on the transgene was deduced by quantifying band intensities in gel electrophoresis pictures (ImageJ software), and calculating the lower/upper ratio. Data, which were normalized by the lower/upper ratio in input samples, derive from at least two independent ChIP experiments, with two PCR/XbaI/electrophoresis analyses in each case. * P

    Article Snippet: ChIP-derived DNA was amplified in a 30 µL PCR reaction containing 1x DreamTaq Buffer (Fermentas GmbH, Leon-Rot, Germany), 200 µM of each dNTP (Takara, Shiga, Japan), 1% of DMSO (Merck Millipore, Darmstadt, Germany), 5 µM of each primer, and 25 units of DreamTaq Polymerase (Fermentas).

    Techniques: In Vitro, Methylation, DNA Methylation Assay, Sequencing, Amplification, Chromatin Immunoprecipitation, Nucleic Acid Electrophoresis, Software, Polymerase Chain Reaction, Electrophoresis

    DNA demethylation induces reversal of histone marks in MAGEA1/hph . A , Schematic outline of the derivation of the H r population and H r clone 1 from MZ2-MEL.TrHM cells (see reference [24] for details). MZ2-MEL.TrHM cells were repeatedly tranfected with antisense oligonucleotides directed against DNMT1 ( DNMT1-AS ) during 7 days, and were thereafter transferred into medium containing hygromycin. After 9 days of hygromycin selection, a resistant population emerged (H r population), and a clone (H r clone 1) was isolated from this population by limiting dilution. The H r population and H r clone 1 were subsequently cultured without hygromycin selection. B , The mRNA expression level (ratio to 10 4 ACTINB ) and 5′-region DNA methylation status (% methylated CpGs) of the MAGEA1/hph transgene were determined in MZ2-MEL.TrHM cells, the H r population and H r clone 1 by qRT-PCR and bisulfite sequencing, respectively. C , ChIP-qPCR was used to evaluate enrichment of H3K9me2 within the MAGEA1/hph transgene in the three groups of cells (see text for details). Fold enrichment levels were obtained by reporting the MAGEA1 5′-region enrichment values to that of the GAPDH 5′-region in the same sample. Data represent the mean (± sem) of two to three ChIP experiments, with two duplicate qPCR measurements in each case. *** P

    Journal: PLoS ONE

    Article Title: Epigenetic Hierarchy within the MAGEA1 Cancer-Germline Gene: Promoter DNA Methylation Dictates Local Histone Modifications

    doi: 10.1371/journal.pone.0058743

    Figure Lengend Snippet: DNA demethylation induces reversal of histone marks in MAGEA1/hph . A , Schematic outline of the derivation of the H r population and H r clone 1 from MZ2-MEL.TrHM cells (see reference [24] for details). MZ2-MEL.TrHM cells were repeatedly tranfected with antisense oligonucleotides directed against DNMT1 ( DNMT1-AS ) during 7 days, and were thereafter transferred into medium containing hygromycin. After 9 days of hygromycin selection, a resistant population emerged (H r population), and a clone (H r clone 1) was isolated from this population by limiting dilution. The H r population and H r clone 1 were subsequently cultured without hygromycin selection. B , The mRNA expression level (ratio to 10 4 ACTINB ) and 5′-region DNA methylation status (% methylated CpGs) of the MAGEA1/hph transgene were determined in MZ2-MEL.TrHM cells, the H r population and H r clone 1 by qRT-PCR and bisulfite sequencing, respectively. C , ChIP-qPCR was used to evaluate enrichment of H3K9me2 within the MAGEA1/hph transgene in the three groups of cells (see text for details). Fold enrichment levels were obtained by reporting the MAGEA1 5′-region enrichment values to that of the GAPDH 5′-region in the same sample. Data represent the mean (± sem) of two to three ChIP experiments, with two duplicate qPCR measurements in each case. *** P

    Article Snippet: ChIP-derived DNA was amplified in a 30 µL PCR reaction containing 1x DreamTaq Buffer (Fermentas GmbH, Leon-Rot, Germany), 200 µM of each dNTP (Takara, Shiga, Japan), 1% of DMSO (Merck Millipore, Darmstadt, Germany), 5 µM of each primer, and 25 units of DreamTaq Polymerase (Fermentas).

    Techniques: Selection, Isolation, Cell Culture, Expressing, DNA Methylation Assay, Methylation, Quantitative RT-PCR, Methylation Sequencing, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Histone changes associated with the activation of gene MAGEA1 in melanoma cell lines. A , MAGEA1 mRNA expression levels (upper panel) and 5′-region DNA methylation levels (lower panel) were evaluated in three non-expressing cell lines (HFF2-hTERT, SK-MEL-23 and EB16-MEL) as well as in three expressing cell lines (MZ2-MEL3.1, BB74-MEL and Mi13443-MEL). Values represent the mean (± sem) of two independent qRT-PCR or qMS-PCR experiments, each in duplicate. B , ChIP-quantitative PCR was applied to the same cell lines to evaluate enrichment of the indicated histone modifications within either the MAGEA1 5′-region or the GAPDH promoter (representing a ubiquitously active promoter). Data derive from at least two independent ChIP experiments, with two duplicate qPCR measures in each case.

    Journal: PLoS ONE

    Article Title: Epigenetic Hierarchy within the MAGEA1 Cancer-Germline Gene: Promoter DNA Methylation Dictates Local Histone Modifications

    doi: 10.1371/journal.pone.0058743

    Figure Lengend Snippet: Histone changes associated with the activation of gene MAGEA1 in melanoma cell lines. A , MAGEA1 mRNA expression levels (upper panel) and 5′-region DNA methylation levels (lower panel) were evaluated in three non-expressing cell lines (HFF2-hTERT, SK-MEL-23 and EB16-MEL) as well as in three expressing cell lines (MZ2-MEL3.1, BB74-MEL and Mi13443-MEL). Values represent the mean (± sem) of two independent qRT-PCR or qMS-PCR experiments, each in duplicate. B , ChIP-quantitative PCR was applied to the same cell lines to evaluate enrichment of the indicated histone modifications within either the MAGEA1 5′-region or the GAPDH promoter (representing a ubiquitously active promoter). Data derive from at least two independent ChIP experiments, with two duplicate qPCR measures in each case.

    Article Snippet: ChIP-derived DNA was amplified in a 30 µL PCR reaction containing 1x DreamTaq Buffer (Fermentas GmbH, Leon-Rot, Germany), 200 µM of each dNTP (Takara, Shiga, Japan), 1% of DMSO (Merck Millipore, Darmstadt, Germany), 5 µM of each primer, and 25 units of DreamTaq Polymerase (Fermentas).

    Techniques: Activation Assay, Expressing, DNA Methylation Assay, Quantitative RT-PCR, Polymerase Chain Reaction, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    DGGE analysis of nested 160-bp β-proteobacterial ammonia oxidizer 16S rDNA sequences amplified from DNA extracted from Loch Duich marine sediments and reference sequences retrieved from Loch Duich sediments by cloning and by sequencing of excised DGGE bands. Lanes: EL, environmental library (DGGE sequences excised and reamplified from 357f-GC plus 518r 16S rDNA PCR products); CL, clone library (βAMO161f plus βAMO1301 clone sequences retrieved from Loch Duich sediments and reamplified with 357f-GC plus 518r for DGGE analysis); 1 to 40, depth profile of Loch Duich 16S rDNA 357f-GC plus 518r PCR products. Clone sequences shown in lane CL are (from top to bottom) LD1-B6, LD1-B37, LD1-A40, LD1-A3, LD1-A1, LD1-A2, LD1-B20, LD1-B10, LD1-B28, LD1-A10, LD1-A15, LD1-B9, and LD1-A20; DGGE excised sequences shown in lane EL are (from top to bottom) LD1-env-A12, LD1-env-B12, LD1-env-B11, LD1-env-B5, LD1-env-A8, LD1-env-A5, LD1-env-A1, and LD1-env-A2. Arrows (right) mark the prominent bands as referred to in the text. No sequence was generated from band X when it was excised and reamplified.

    Journal: Applied and Environmental Microbiology

    Article Title: Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments

    doi: 10.1128/AEM.69.3.1359-1371.2003

    Figure Lengend Snippet: DGGE analysis of nested 160-bp β-proteobacterial ammonia oxidizer 16S rDNA sequences amplified from DNA extracted from Loch Duich marine sediments and reference sequences retrieved from Loch Duich sediments by cloning and by sequencing of excised DGGE bands. Lanes: EL, environmental library (DGGE sequences excised and reamplified from 357f-GC plus 518r 16S rDNA PCR products); CL, clone library (βAMO161f plus βAMO1301 clone sequences retrieved from Loch Duich sediments and reamplified with 357f-GC plus 518r for DGGE analysis); 1 to 40, depth profile of Loch Duich 16S rDNA 357f-GC plus 518r PCR products. Clone sequences shown in lane CL are (from top to bottom) LD1-B6, LD1-B37, LD1-A40, LD1-A3, LD1-A1, LD1-A2, LD1-B20, LD1-B10, LD1-B28, LD1-A10, LD1-A15, LD1-B9, and LD1-A20; DGGE excised sequences shown in lane EL are (from top to bottom) LD1-env-A12, LD1-env-B12, LD1-env-B11, LD1-env-B5, LD1-env-A8, LD1-env-A5, LD1-env-A1, and LD1-env-A2. Arrows (right) mark the prominent bands as referred to in the text. No sequence was generated from band X when it was excised and reamplified.

    Article Snippet: Individual reagents and their concentrations were as follows: 1× PCR buffer (Bioline), 1 U of BioTaq DNA polymerase (Bioline), 1.5 mM MgCl2 , each primer at a concentration of 0.2 μM, and each deoxynucleoside triphosphate dNTP (Bioline) at a concentration of 250 μM.

    Techniques: Denaturing Gradient Gel Electrophoresis, Amplification, Clone Assay, Sequencing, Polymerase Chain Reaction, Generated

    DGGE analysis of nested 160-bp Planctomycetales-Verrucomicrobia 16S rDNA sequences amplified from DNA extracted from Loch Duich marine sediments and reference sequences retrieved from Loch Duich sediments by cloning and sequencing of excised bands from DGGE gels. Lanes EL, environmental library (DGGE sequences excised and reamplified from 357f-GC plus 518r 16S rDNA PCR products); CL, clone library (PV clone sequences retrieved from Loch Duich sediments, reamplified with 357f-GC plus 518r for DGGE analysis); 1 to 36, depth profile 16S rDNA PCR products of Loch Duich sediment samples. Clone sequences in lane CL are (from top to bottom) LD1-PA42, LD1-PA15, LD1-PB1, LD1-PA13, LD1-PA26, LD1-PB2, LD1-PA40, LD1-PA32, LD1-PA16, LD1-PB20, LD1-PA30, LD1-PA20, LD1-PA21, LD1-PB12, LD1-PA11, LD1-PB3, LD1-PA50, LD1-PA34, and LD1-27; DGGE excised sequences in lane EL are (from top to bottom) LD1-env-P8, LD1-env-P7, LD1-env-P6, LD1-env-P1, LD1-env-P4, LD1-env-P3, LD1-env-P2, and LD1-env-P5. No sequence was generated from the band marked with an arrow when it was excised and reamplified.

    Journal: Applied and Environmental Microbiology

    Article Title: Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments

    doi: 10.1128/AEM.69.3.1359-1371.2003

    Figure Lengend Snippet: DGGE analysis of nested 160-bp Planctomycetales-Verrucomicrobia 16S rDNA sequences amplified from DNA extracted from Loch Duich marine sediments and reference sequences retrieved from Loch Duich sediments by cloning and sequencing of excised bands from DGGE gels. Lanes EL, environmental library (DGGE sequences excised and reamplified from 357f-GC plus 518r 16S rDNA PCR products); CL, clone library (PV clone sequences retrieved from Loch Duich sediments, reamplified with 357f-GC plus 518r for DGGE analysis); 1 to 36, depth profile 16S rDNA PCR products of Loch Duich sediment samples. Clone sequences in lane CL are (from top to bottom) LD1-PA42, LD1-PA15, LD1-PB1, LD1-PA13, LD1-PA26, LD1-PB2, LD1-PA40, LD1-PA32, LD1-PA16, LD1-PB20, LD1-PA30, LD1-PA20, LD1-PA21, LD1-PB12, LD1-PA11, LD1-PB3, LD1-PA50, LD1-PA34, and LD1-27; DGGE excised sequences in lane EL are (from top to bottom) LD1-env-P8, LD1-env-P7, LD1-env-P6, LD1-env-P1, LD1-env-P4, LD1-env-P3, LD1-env-P2, and LD1-env-P5. No sequence was generated from the band marked with an arrow when it was excised and reamplified.

    Article Snippet: Individual reagents and their concentrations were as follows: 1× PCR buffer (Bioline), 1 U of BioTaq DNA polymerase (Bioline), 1.5 mM MgCl2 , each primer at a concentration of 0.2 μM, and each deoxynucleoside triphosphate dNTP (Bioline) at a concentration of 250 μM.

    Techniques: Denaturing Gradient Gel Electrophoresis, Amplification, Clone Assay, Sequencing, Polymerase Chain Reaction, Generated

    Detecting murine DNA by IAP PCR. PCR products were analyzed on 1.5% agarose gels containing ethidium bromide. (A) Sensitivity of the IAP PCR assay was determined by performing PCRs on titrations of EL4 murine cell line DNA in a background of 200 ng LNCaP DNA. One murine cell equivalent (1 eq) indicates 6 pg of EL4 DNA. XMRV-infected LNCaP (iLNCaP) and uninfected LNCaP (uLNCaP) were included as controls. (B) Screening results for 17 HIV-1 + patient samples. Arrow points to sample 103219, which tested positive for XMRV by non-nested gag PCR. (m) 100 base pair molecular weight marker, (EL4) 6 pg of murine EL4 cell line DNA without a background of human DNA.

    Journal: PLoS ONE

    Article Title: Absence of XMRV in Peripheral Blood Mononuclear Cells of ARV-Treatment Na?ve HIV-1 Infected and HIV-1/HCV Coinfected Individuals and Blood Donors

    doi: 10.1371/journal.pone.0031398

    Figure Lengend Snippet: Detecting murine DNA by IAP PCR. PCR products were analyzed on 1.5% agarose gels containing ethidium bromide. (A) Sensitivity of the IAP PCR assay was determined by performing PCRs on titrations of EL4 murine cell line DNA in a background of 200 ng LNCaP DNA. One murine cell equivalent (1 eq) indicates 6 pg of EL4 DNA. XMRV-infected LNCaP (iLNCaP) and uninfected LNCaP (uLNCaP) were included as controls. (B) Screening results for 17 HIV-1 + patient samples. Arrow points to sample 103219, which tested positive for XMRV by non-nested gag PCR. (m) 100 base pair molecular weight marker, (EL4) 6 pg of murine EL4 cell line DNA without a background of human DNA.

    Article Snippet: A final PCR reaction volume of 50 µl contained: 250 ng DNA, 5 µl GeneAmp 10× PCR Gold Buffer (Applied Biosystems), 2.5 mM MgCl2 , 800 µM dNTPs, 0.3 µM of each forward and reverse primer, and 1.5 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

    Techniques: Polymerase Chain Reaction, Infection, Molecular Weight, Marker

    Sensitivity analysis of XMRV PCR assays. PCR products were analyzed on agarose gels containing ethidium bromide. (A) Non-nested PCR assays targeting the XMRV env gene (top panel) and the gag gene (bottom panel), and (B) a nested PCR assay targeting the XMRV env gene were evaluated for their ability to detect either (A) provirus in XMRV-infected PNT1A cell DNA or (B) provirus in XMRV-infected LNCaP cell DNA diluted in uninfected cell DNA. Dilutions of infected cells in uninfected cells are indicated by ratios, i.e. 1∶10 4 indicates one infected cell diluted in 10 4 uninfected cells. (m) 100 base pair molecular weight marker, (H 2 O) water used in place of DNA template as a negative control, (u) uninfected PNT1A DNA used as template for negative control.

    Journal: PLoS ONE

    Article Title: Absence of XMRV in Peripheral Blood Mononuclear Cells of ARV-Treatment Na?ve HIV-1 Infected and HIV-1/HCV Coinfected Individuals and Blood Donors

    doi: 10.1371/journal.pone.0031398

    Figure Lengend Snippet: Sensitivity analysis of XMRV PCR assays. PCR products were analyzed on agarose gels containing ethidium bromide. (A) Non-nested PCR assays targeting the XMRV env gene (top panel) and the gag gene (bottom panel), and (B) a nested PCR assay targeting the XMRV env gene were evaluated for their ability to detect either (A) provirus in XMRV-infected PNT1A cell DNA or (B) provirus in XMRV-infected LNCaP cell DNA diluted in uninfected cell DNA. Dilutions of infected cells in uninfected cells are indicated by ratios, i.e. 1∶10 4 indicates one infected cell diluted in 10 4 uninfected cells. (m) 100 base pair molecular weight marker, (H 2 O) water used in place of DNA template as a negative control, (u) uninfected PNT1A DNA used as template for negative control.

    Article Snippet: A final PCR reaction volume of 50 µl contained: 250 ng DNA, 5 µl GeneAmp 10× PCR Gold Buffer (Applied Biosystems), 2.5 mM MgCl2 , 800 µM dNTPs, 0.3 µM of each forward and reverse primer, and 1.5 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

    Techniques: Polymerase Chain Reaction, Nested PCR, Infection, Molecular Weight, Marker, Negative Control

    Screening for XMRV in patient PBMCs by PCR. PCR products were analyzed on agarose gels containing ethidium bromide. (A) Representative gels for non-nested env (top panel) and non-nested gag (bottom panel) PCRs are shown containing a set of three replicates for each of 5 HIV-1 + patient samples. A yellow arrow indicates the sole PCR band, from patient 103219, found to be comprised of XMRV DNA by sequencing. (B) A representative gel for nested env PCR is shown for the same 5 HIV-1 + patient samples depicted in (A). Vertical black arrows in (A) and (B) indicate lanes from patient 103219 containing either (A, bottom panel) a band comprised of XMRV sequence or (B) a band of the expected mobility for the target sequence. (m) 100 base pair molecular weight marker, (1∶10 4 ) DNA from one infected cell diluted in DNA from 10 4 uninfected cells used as template for positive control.

    Journal: PLoS ONE

    Article Title: Absence of XMRV in Peripheral Blood Mononuclear Cells of ARV-Treatment Na?ve HIV-1 Infected and HIV-1/HCV Coinfected Individuals and Blood Donors

    doi: 10.1371/journal.pone.0031398

    Figure Lengend Snippet: Screening for XMRV in patient PBMCs by PCR. PCR products were analyzed on agarose gels containing ethidium bromide. (A) Representative gels for non-nested env (top panel) and non-nested gag (bottom panel) PCRs are shown containing a set of three replicates for each of 5 HIV-1 + patient samples. A yellow arrow indicates the sole PCR band, from patient 103219, found to be comprised of XMRV DNA by sequencing. (B) A representative gel for nested env PCR is shown for the same 5 HIV-1 + patient samples depicted in (A). Vertical black arrows in (A) and (B) indicate lanes from patient 103219 containing either (A, bottom panel) a band comprised of XMRV sequence or (B) a band of the expected mobility for the target sequence. (m) 100 base pair molecular weight marker, (1∶10 4 ) DNA from one infected cell diluted in DNA from 10 4 uninfected cells used as template for positive control.

    Article Snippet: A final PCR reaction volume of 50 µl contained: 250 ng DNA, 5 µl GeneAmp 10× PCR Gold Buffer (Applied Biosystems), 2.5 mM MgCl2 , 800 µM dNTPs, 0.3 µM of each forward and reverse primer, and 1.5 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

    Techniques: Polymerase Chain Reaction, DNA Sequencing, Sequencing, Molecular Weight, Marker, Infection, Positive Control

    PCR amplification of total DNA of Arabidopsis

    Journal: Journal of Virology

    Article Title: Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿ †

    doi: 10.1128/JVI.00955-10

    Figure Lengend Snippet: PCR amplification of total DNA of Arabidopsis

    Article Snippet: The total volume of each PCR mix was 20 μl and contained 1 μl of DNA template, 2 μl 10× PCR buffer (TaKaRa), 0.4 μl of deoxynucleoside triphosphate (dNTP) mix (10 mM [each dNTP]), 0.2 μl of each primer (20 μM), and 1 unit of Taq DNA polymerase.

    Techniques: Polymerase Chain Reaction, Amplification

    PCR amplification of Rbcl after cutting using HaeIII and BlgII enzymes, where E1 to E3 different Egyptian cotton varieties A1 to A3 are different American cotton varieties and the L is lab’s cotton. The white arrows show some bands differentiate between Egyptian and American genotypes:

    Journal: bioRxiv

    Article Title: A rapid method for DNA extraction of cotton mature fiber suitable for PCR fingerprinting

    doi: 10.1101/529305

    Figure Lengend Snippet: PCR amplification of Rbcl after cutting using HaeIII and BlgII enzymes, where E1 to E3 different Egyptian cotton varieties A1 to A3 are different American cotton varieties and the L is lab’s cotton. The white arrows show some bands differentiate between Egyptian and American genotypes:

    Article Snippet: For PCR amplification and sequencing of RbcL, the primer combination was Forward primer: 5′-ATGTCACCACAAACAGAGACTAAAGC-3′and Reverse primer: 5′-TCGCATGTACCTGCAGTAGC-3′.

    Techniques: Polymerase Chain Reaction, Amplification

    The PCR products of Rbcl DNA-Barcode for the Lab’s cotton (L) Egyptian (E1, E2, E3) and American (A1, A2, A3) varieties using the DNA isolated from fiber.

    Journal: bioRxiv

    Article Title: A rapid method for DNA extraction of cotton mature fiber suitable for PCR fingerprinting

    doi: 10.1101/529305

    Figure Lengend Snippet: The PCR products of Rbcl DNA-Barcode for the Lab’s cotton (L) Egyptian (E1, E2, E3) and American (A1, A2, A3) varieties using the DNA isolated from fiber.

    Article Snippet: For PCR amplification and sequencing of RbcL, the primer combination was Forward primer: 5′-ATGTCACCACAAACAGAGACTAAAGC-3′and Reverse primer: 5′-TCGCATGTACCTGCAGTAGC-3′.

    Techniques: Polymerase Chain Reaction, Isolation

    Gel electrophoresis (2% TAE-agarose gel) showing amplified DNA of potentially contaminated samples (specific bands of approximately 500-bp length). Lanes: 1, 100-bp marker; 2, zymolyase, contaminated lot; 3, zymolyase, contaminated lot, 1:10 dilution; 4, 10× buffer from digoxigenin (Dig)-labeling kit (Boehringer Mannheim), contaminated lot; 5, 10× buffer from Dig-labeling kit (Boehringer Mannheim), contaminated lot; 6, zymolyase, regular lot, not contaminated; 7, proteinase K, regular lot, not contaminated; 8, lyticase, contaminated lot; 9, lysing enzyme extracted from T. harzianum ; 10, positive control, A. fumigatus DNA, extracted from 10 3 CFU; 11, negative control of the extraction; and 12, negative control of the PCR.

    Journal: Journal of Clinical Microbiology

    Article Title: Contaminations Occurring in Fungal PCR Assays

    doi:

    Figure Lengend Snippet: Gel electrophoresis (2% TAE-agarose gel) showing amplified DNA of potentially contaminated samples (specific bands of approximately 500-bp length). Lanes: 1, 100-bp marker; 2, zymolyase, contaminated lot; 3, zymolyase, contaminated lot, 1:10 dilution; 4, 10× buffer from digoxigenin (Dig)-labeling kit (Boehringer Mannheim), contaminated lot; 5, 10× buffer from Dig-labeling kit (Boehringer Mannheim), contaminated lot; 6, zymolyase, regular lot, not contaminated; 7, proteinase K, regular lot, not contaminated; 8, lyticase, contaminated lot; 9, lysing enzyme extracted from T. harzianum ; 10, positive control, A. fumigatus DNA, extracted from 10 3 CFU; 11, negative control of the extraction; and 12, negative control of the PCR.

    Article Snippet: Detailed and repeated serial analysis of all components of the PCR mixture (nucleotides, primers, water, magnesium chloride, 10× buffer, and Taq polymerase) showed a positive specific band only in the 10× PCR buffer supplied by Boehringer Mannheim.

    Techniques: Nucleic Acid Electrophoresis, Agarose Gel Electrophoresis, Amplification, Marker, Labeling, Positive Control, Negative Control, Polymerase Chain Reaction

    Gel images illustrating the quality of RNA extracts and their suitability for RT-PCR. In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii nifH RT-PCR products (370 bp; 2% agarose).

    Journal: Applied and Environmental Microbiology

    Article Title: mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil

    doi: 10.1128/AEM.69.4.1928-1935.2003

    Figure Lengend Snippet: Gel images illustrating the quality of RNA extracts and their suitability for RT-PCR. In each panel the arrows on the left indicate the position(s) of the expected band(s) on the gel. The arrowheads on the right indicate the positions of the 1,636- and 517- or 506-bp fragments of the molecular weight marker. Lane 1, total nucleic acid extract from reference soil; lane 2, total RNA extract from reference (Ref.) soil; lanes 4 to 9, duplicate SC −N RNA extracts (lanes 4 and 5, day 2; lanes 6 and 7, day 3; lanes 8 and 9, day 7); lanes 11 and 12, LC −N liquid culture RNA extracts from day 2; lanes 3 and 10, 1-kb DNA marker. (A) Six microliters (equivalent to RNA from 0.1 g of soil or 0.4 ml of liquid culture) of nucleic acid extract sample (2% agarose). (B) Six-microliter portions of 50-μl bacterial SSU rRNA RT-PCR products (1,070 bp; 1% agarose). Reference soil extracts were used undiluted, and all other samples were diluted to a concentration of 3 ng μl −1 prior to RT. (C) Six-microliter portions of 50-μl bacterial SSU rRNA PCR products used to test for DNA contamination (1% agarose). The reaction mixtures were identical to those shown in panel B except that they did not contain AMV reverse transcriptase in the RT step. (D) Six-microliter portions of 50-μl A. vinelandii nifH RT-PCR products (370 bp; 2% agarose).

    Article Snippet: The reaction mixture (final volume, 50 μl) contained 0.8 mM MgCl2 , each deoxynucleoside triphosphate at a concentration of 0.2 mM, 0.2 μM primer nifH-g1-forB, 0.2 μM primer nifH-g1-rev, 5 mg of bovine serum albumin per ml, and 1× PCR buffer (Amersham Biosciences).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Molecular Weight, Marker, Concentration Assay, Polymerase Chain Reaction

    Relationship of A. vinelandii nifH RT-PCR product intensity quantified from ethidium bromide-stained agarose gels to specific N fixation activity determined by acetylene reduction. (A) Liquid culture treatments. (B) Soil culture treatments. The correlation coefficients of the exponential fitting functions were highly significant ( P = 0.01) for both treatment types.

    Journal: Applied and Environmental Microbiology

    Article Title: mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil

    doi: 10.1128/AEM.69.4.1928-1935.2003

    Figure Lengend Snippet: Relationship of A. vinelandii nifH RT-PCR product intensity quantified from ethidium bromide-stained agarose gels to specific N fixation activity determined by acetylene reduction. (A) Liquid culture treatments. (B) Soil culture treatments. The correlation coefficients of the exponential fitting functions were highly significant ( P = 0.01) for both treatment types.

    Article Snippet: The reaction mixture (final volume, 50 μl) contained 0.8 mM MgCl2 , each deoxynucleoside triphosphate at a concentration of 0.2 mM, 0.2 μM primer nifH-g1-forB, 0.2 μM primer nifH-g1-rev, 5 mg of bovine serum albumin per ml, and 1× PCR buffer (Amersham Biosciences).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Staining, Activity Assay

    Cell density, nitrogen fixation activity, and intensity of nifH mRNA expression plotted against time. (A) Cell counts for DAPI-stained bacteria in liquid culture and soil. (B) Nitrogen fixation activity determined by the acetylene reduction method with liquid cultures and soil. Upper plot, SC −N and LC −N ; lower plot (reduced scale), SC +N and LC +N . (C) Intensities of nifH mRNA RT-PCR products determined by image analyses of gel images. Left panel, liquid culture treatments; right panel, soil culture treatments. The error bars in panels A and B indicate the standard errors of the measurements. Symbols: ▪, LC +N or SC +N replicate 1; •, LC +N or SC +N replicate 2; □, LC −N or SC −N replicate 1; ○, LC −N or SC −N replicate 2; ×, LC control or SC control. n.d., not determined.

    Journal: Applied and Environmental Microbiology

    Article Title: mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil

    doi: 10.1128/AEM.69.4.1928-1935.2003

    Figure Lengend Snippet: Cell density, nitrogen fixation activity, and intensity of nifH mRNA expression plotted against time. (A) Cell counts for DAPI-stained bacteria in liquid culture and soil. (B) Nitrogen fixation activity determined by the acetylene reduction method with liquid cultures and soil. Upper plot, SC −N and LC −N ; lower plot (reduced scale), SC +N and LC +N . (C) Intensities of nifH mRNA RT-PCR products determined by image analyses of gel images. Left panel, liquid culture treatments; right panel, soil culture treatments. The error bars in panels A and B indicate the standard errors of the measurements. Symbols: ▪, LC +N or SC +N replicate 1; •, LC +N or SC +N replicate 2; □, LC −N or SC −N replicate 1; ○, LC −N or SC −N replicate 2; ×, LC control or SC control. n.d., not determined.

    Article Snippet: The reaction mixture (final volume, 50 μl) contained 0.8 mM MgCl2 , each deoxynucleoside triphosphate at a concentration of 0.2 mM, 0.2 μM primer nifH-g1-forB, 0.2 μM primer nifH-g1-rev, 5 mg of bovine serum albumin per ml, and 1× PCR buffer (Amersham Biosciences).

    Techniques: Activity Assay, Expressing, Staining, Reverse Transcription Polymerase Chain Reaction